Solution Structure of a Steroid−DNA Complex with Cholic Acid Residues Sealing the Termini of a Watson−Crick Duplex

Abstract

The three-dimensional structure of a covalent hybrid between cholic acid and the self-complementary DNA hexamer 5'-TGCGCA-3' was solved via two-dimensional NMR and restrained torsion angle molecular dynamics. In the complex, refined to a pairwise rmsd of 0.64 A, the steroid binds to the terminal T:A base pairs via extensive van der Waals contacts but without any hydrogen bonds or detectable dipole-dipole interactions. The contacts involve the methyl groups as well as one edge of the streoid's sterane skeleton and both nucleobases and the deoxyriboses of the terminal base pair of the DNA. The surprising shape complementarity between steroid and the undisturbed DNA termini explains the increase in fidelity and affinity observed for hybridization probes bearing bile acid residues. Since the hydroxyl groups of the steroid do not contribute to the binding of the DNA, they may be derivatized, potentially giving access to a new class of specific binders for blunt ends of Watson-Crick duplexes.

Pyrenylmethyldeoxyadenosine: A 3′‐Cap for Universal DNA Hybridization Probes

“…The "wobble hypothesis" [4] has helped to explain the degeneracy of the genetic code, but does not allow for more than qualitative predictions outside the ribosome, and the fidelity of base pairing, particularly at the termini, remains difficult-to-predict. [5] Ligands that enhance stability and base-pairing fidelity at the termini when covalently attached to one of the duplex-forming strands have been identified, but the structural diversity among these ligands, ranging from steroids [6] to aromatic systems like quinolones, [7,8] and stilbenes, [9,10] has made it difficult to draw general conclusions.…”

“…That PAHs may do neither of the two, but have a general fidelity-decreasing effect is not obvious. Here we report on such an effect that we encountered when testing small molecule ligands covalently attached to the termini of oligonucleotides (Figure 1), [6,10,17,18] as part of a project aimed at generating high fidelity hybridization probes featuring molecular caps at the 3'-terminus. [19] …”

Tuning the Reaction Site for Enzyme‐Free Primer‐Extension Reactions through Small Molecule Substituents

“…Further, there is no obvious shape complementarity that prevents incorporation of mismatched nucleotides. Except for the trimethoxystilbene and the cholic acid residue, which are known to "gauge" terminal base pairs through molecular interactions with terminal base pairs by packing against the deoxyribose of the target nucleotide, [22,24] neither cap has an obvious structural feature that prevents the formation of wobble base pairs and other possible mismatches. Neither the trimethoxystilbene nor the cholic acid residue is among the most selectivity-inducing caps in our study.…”

Polyaza Crown Ethers as Non‐Nucleosidic Building Blocks in DNA Conjugates: Synthesis and Remarkable Stabilization of dsDNA

“…15 Most notably, steroids such as cholic acid and related compounds stabilize dsDNA when attached in a terminal position, but none of them has been designed as a building block for pore‐forming compounds 16. 17 DNA–lipid conjugates (e.g., cholesteryl conjugates) have for a long time been known to facilitate the insertion and transport of ssDNA, and more recently siRNA, through biological membranes 18. 3…”